Hi Sergei,
I don't think that there is a program available to do what you want, but
I think that the tools are there for you to make one. The biggest
challenge you will have is keeping the mathematics straight!
So, if you start off with something like the DiffractionImage library,
this will help with reading in the diffraction images - contact Francois
Remacle for this one ([log in to unmask]) - you will need to know the
beam centre, wavelength and detector distance *exactly* for this to be
useful. Well, more exactly than is normal in image headers ;o)
Next you will need something which can render the 3D density that you
will generate - I would google "voxel" and see what you can come up
with. I vaguely remember some libraries for this kind of thing available
in C/C++. Common uses are medical imaging.
Now comes the tricky bit. You will need to work through each image and
for each pixel add the approptiate constant times the pixel value to the
"right" voxel given by the diffraction geometry. The calculations for
this appear in most crystallography texts, though I expect computing
said constant will be non-trivial. The constant will correct for the
"volume" of the pixel in reciprical space, determined by the position on
the detector face and the oscillation angle.
After that you should be about done.
Oh, and you might want to do this on rather a large computer if you
intend to get a high resolution representation of each reflection on all
of the images. If you are wanting a voxel cube 1000 pixels to a side
(say) as int*2 (say) this is a 2GB before you have read in your first
image. Without some kind of prediction and shoeboxing (as goes on inside
XDS, for instance) you won't be able to avoid this.
Good luck,
Graeme
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Sergei Strelkov
Sent: 12 July 2007 16:29
To: [log in to unmask]
Subject: Re: [ccp4bb] Program to 'visualize' the reciprocal space ?
Many thanks to good people who have responded to my message! Apparently
I have to apologize for not formulating my question clearly enough. Here
is more explanation.
According to Ewald construction, diffraction images collected by
oscillation method correspond to thin 'curved' slices of the reciprocal
space. What I am looking for is a program to generate the reciprocal
space (as a 3D map) from these 'slices' directly, *without* any indexing
or integration of I's. This is a simple purely geometrical calculation.
This is *not* anything routinely done for normal high-quality crystal
data.
For a good dataset, such a conversion should simply yield a lattice with
distinct points. For our partially-ordered crystals, this should help us
visualizing the actual 'shapes' of our reflections (many of them are
smeared/overlapping).
My guess that folks working with semi-ordered systems, such as liquid
crystals or lipid bilayers, should have some programs like that...
any ideas?
Thank you again,
Sergei.
> Dear All,
>
> we are dealing with a difficult case of a 'partially ordered' protein
> crystal.
> Here it would be very useful to view the reciprocal space as a 3D map.
> Is anyone aware of a program that would convert standard oscillation
> data (one-degree frames, mar225) into such a map? What we need is a
> direct conversion.
> There is a program in CCP4 that is able to 'visualize' the reciprocal
> space, but it requires hkl's as input.
>
> Thank you,
> Sergei Strelkov
>
--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Catholic University of Leuven
Campus Gasthuisberg, O&N2 Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 33 08 45 Fax: +32 16 32 34 69
Mobile: +32 486 29 41 32
E-mail: [log in to unmask]
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
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